TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

Area of Science:

• Bioinformatics
• Computational Biology
• Systematics

Background:

• Large volumes of DNA sequence data lack taxonomic identification, complicating curation and diversity analysis.
• Phylogenetic tree construction is crucial for classifying and understanding evolutionary relationships within these datasets.
• Manually segregating sequences based on tree topology is time-consuming and challenging for extensive data.

Purpose of the Study:

• To develop an automated method for sorting DNA sequences based on phylogenetic tree structures.
• To streamline the process of taxonomic curation and molecular diversity characterization for large sequence datasets.
• To provide a user-friendly tool that integrates with existing phylogenetic visualization software.

Main Methods:

• Development of a Perl script named TREE2FASTA.
• Utilizing interactive tree visualization software (FigTree) for sequence selection.
• Implementing point-and-click color selection and annotation of tree leaves.
• Enabling segregation of FASTA-formatted sequence data into separate files based on tree topology.

Main Results:

• TREE2FASTA effectively automates the segregation of FASTA sequences from phylogenetic trees.
• The script supports both simple and nested segregation designs for complex data organization.
• It facilitates the simultaneous preparation of multiple, potentially overlapping, datasets.
• The tool significantly expedites the sorting process compared to manual methods.

Conclusions:

• TREE2FASTA offers an efficient solution for managing and curating large, unannotated DNA sequence datasets.
• The script enhances the utility of exploratory phylogenetic analyses in systematics and biodiversity research.
• This tool aids researchers in identifying cryptic species and performing molecular diversity assessments more effectively.